GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TPP_enzyme_N - Thiamine pyrophosphate enzyme N-terminal TPP binding domain
Pfam: PF02776 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0254
Length: 172
Sequences: 7174
Seq/Len: 41.71
HH_delta: -0.056 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
52_A82_G1.714484.077
17_T64_R1.222782.908
45_V51_A1.027652.444
118_S121_R1.020062.426
18_H41_R1.015662.415
5_E33_A0.971252.310
70_V79_A0.944862.247
97_T156_Y0.922842.194
9_E13_A0.912872.171
12_K39_G0.912092.169
77_T81_T0.902412.146
115_D118_S0.888572.113
83_L95_V0.869912.069
56_D60_R0.855232.034
45_V54_M0.823881.959
14_N141_D0.818591.947
94_L144_F0.769981.831
139_A157_L0.769251.829
31_L42_F0.755621.797
21_G42_F0.74741.777
12_K37_S0.744611.771
132_S135_D0.732321.741
10_A141_D0.717741.707
5_E36_K0.701551.668
125_K153_G0.69911.662
9_E12_K0.66221.575
138_E142_R0.648181.541
7_L140_L0.642061.527
87_Y154_P0.641241.525
65_P94_L0.627131.491
94_L147_A0.62421.484
57_G61_A0.61151.454
140_L157_L0.60911.448
56_D85_N0.605581.440
14_N144_F0.605271.439
20_F58_Y0.597481.421
135_D138_E0.584881.391
124_T156_Y0.57121.358
55_A93_V0.564181.342
146_A155_V0.559661.331
139_A142_R0.55691.324
9_E37_S0.556461.323
18_H58_Y0.553761.317
79_A95_V0.542141.289
160_P163_V0.539191.282
102_S162_D0.537771.279
68_V79_A0.534971.272
33_A36_K0.534751.272
76_A97_T0.533261.268
2_T5_E0.530531.262
128_Y139_A0.528761.257
7_L159_I0.525491.250
52_A93_V0.518221.232
52_A79_A0.517921.232
65_P144_F0.510811.215
18_H43_I0.503151.196
10_A14_N0.498361.185
142_R145_R0.497731.184
86_A93_V0.496431.180
130_V139_A0.495571.178
20_F54_M0.492261.171
119_L123_V0.490491.166
53_F82_G0.488861.162
5_E9_E0.487761.160
6_A137_P0.477611.136
3_G133_P0.477121.135
13_A137_P0.474221.128
60_R91_I0.463591.102
17_T63_G0.46151.097
27_N30_L0.461391.097
96_I159_I0.460121.094
19_V34_L0.456321.085
7_L136_L0.451931.075
80_L119_L0.447761.065
56_D91_I0.446971.063
147_A155_V0.446381.061
99_Q158_E0.445971.060
128_Y157_L0.438031.042
94_L143_A0.432311.028
134_D138_E0.432141.028
118_S122_P0.430811.024
130_V136_L0.429261.021
128_Y146_A0.41940.997
10_A140_L0.416720.991
4_A33_A0.416570.991
17_T41_R0.412720.981
141_D145_R0.410390.976
142_R146_A0.403540.960
77_T119_L0.403260.959
3_G136_L0.401010.954
29_P164_Q0.399920.951
56_D86_A0.398030.946
105_E129_R0.393150.935
52_A95_V0.391960.932
108_G111_Q0.389260.926
10_A137_P0.388190.923
77_T80_L0.382930.911
124_T127_S0.382720.910
128_Y142_R0.381480.907
59_A92_P0.379050.901
102_S160_P0.378760.901
127_S156_Y0.378280.900
52_A68_V0.377650.898
126_W139_A0.377410.897
70_V95_V0.377250.897
117_Q129_R0.3770.896
6_A10_A0.37420.890
117_Q121_R0.373230.888
23_P44_P0.372550.886
111_Q114_I0.371920.884
17_T58_Y0.371120.882
32_D35_E0.370990.882
27_N69_I0.368510.876
109_A113_E0.366790.872
120_F127_S0.365760.870
10_A13_A0.365150.868
133_P137_P0.363750.865
49_Q78_N0.363290.864
30_L69_I0.360430.857
107_R111_Q0.35920.854
126_W142_R0.359160.854
90_R151_R0.358790.853
80_L120_F0.358470.852
80_L123_V0.355750.846
27_N31_L0.35570.846
59_A91_I0.355530.845
16_V67_V0.346290.823
83_L93_V0.345960.823
12_K17_T0.345930.823
133_P163_V0.344720.820
8_A37_S0.344590.819
94_L155_V0.343970.818
137_P141_D0.342120.814
117_Q127_S0.341060.811
99_Q105_E0.34070.810
97_T158_E0.33950.807
101_P104_G0.338670.805
126_W146_A0.337940.804
16_V144_F0.337270.802
143_A157_L0.335140.797
58_Y64_R0.334330.795
97_T116_Q0.333440.793
19_V40_I0.323220.769
145_R149_S0.322070.766
3_G6_A0.321620.765
125_K155_V0.319740.760
71_T76_A0.316950.754
159_I164_Q0.315760.751
129_R158_E0.315760.751
125_K151_R0.315020.749
77_T84_A0.314980.749
58_Y62_T0.314710.748
76_A120_F0.308760.734
7_L96_I0.307310.731
70_V76_A0.304570.724
2_T33_A0.303720.722
7_L30_L0.303480.722
116_Q156_Y0.301030.716
68_V95_V0.30020.714
103_A162_D0.298470.710
92_P147_A0.297950.709
5_E37_S0.297680.708
27_N98_G0.296910.706
28_L32_D0.296560.705
78_N81_T0.293040.697
110_F113_E0.292020.694
83_L120_F0.290950.692
11_L68_V0.289920.689
128_Y155_V0.285740.679
16_V68_V0.284360.676
85_N89_D0.284080.676
87_Y125_K0.282280.671
17_T62_T0.281140.669
22_V45_V0.278360.662
19_V67_V0.278180.661
53_F85_N0.277370.660
99_Q129_R0.277240.659
52_A83_L0.275580.655
30_L164_Q0.274750.653
102_S131_T0.274090.652
127_S158_E0.273090.649
116_Q120_F0.271450.645
51_A70_V0.270420.643
21_G31_L0.270140.642
96_I157_L0.270130.642
47_H78_N0.26990.642
126_W143_A0.269880.642
34_L40_I0.269860.642
125_K149_S0.269530.641
119_L122_P0.267550.636
26_G72_S0.267340.636
60_R89_D0.266880.635
87_Y124_T0.266870.635
21_G68_V0.266230.633
26_G71_T0.265350.631
48_E75_G0.26510.630
25_S71_T0.263140.626
130_V160_P0.261070.621
145_R150_G0.260960.621
72_S100_R0.260340.619
30_L159_I0.260060.618
96_I140_L0.259490.617
34_L42_F0.259360.617
56_D82_G0.259270.617
22_V79_A0.2590.616
67_V94_L0.258760.615
55_A67_V0.258610.615
65_P147_A0.257120.611
67_V96_I0.253880.604
130_V157_L0.253050.602
108_G113_E0.252830.601
20_F51_A0.251870.599
11_L16_V0.251350.598
77_T114_I0.25130.598
76_A156_Y0.25110.597
9_E33_A0.250540.596
3_G10_A0.248160.590
14_N94_L0.248130.590
6_A133_P0.247460.588
51_A68_V0.247430.588
14_N140_L0.245930.585
135_D139_A0.245340.583
51_A79_A0.245080.583
136_L140_L0.245060.583
131_T135_D0.244410.581
101_P161_Q0.24360.579
125_K150_G0.242970.578
121_R127_S0.241710.575
125_K152_P0.241360.574
25_S28_L0.239840.570
26_G164_Q0.237150.564
143_A155_V0.237080.564
87_Y153_G0.23680.563
59_A65_P0.236490.562
25_S72_S0.23590.561
20_F55_A0.23560.560
8_A33_A0.235550.560
120_F124_T0.233830.556
18_H64_R0.233710.556
74_P81_T0.232880.554
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
1t9bA0.9942100-0.056
1ybhA0.9942100-0.041
2x7jA0.9942100-0.04
3lq1A0.9942100-0.04
4kgdA0.9884100-0.039
4fegA0.9884100-0.039
1ozhA0.9884100-0.035
3eyaA0.9884100-0.035
2c31A0.9884100-0.031
2q28A0.9884100-0.031

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